| Previous changeset 3:16a1a5ae98e9 (2013-05-08) Next changeset 5:44b2e489e26f (2013-06-24) |
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Commit message:
Uploaded v0.0.4, auto-install Biopython |
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modified:
tools/filters/seq_rename.txt tools/filters/seq_rename.xml |
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added:
tools/filters/repository_dependencies.xml tools/filters/seq_rename.tar.gz |
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| diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/repository_dependencies.xml Mon Jun 24 01:59:15 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<repositories description="This requires Biopython as a dependency."> +<!-- Leave out the tool shed and revision to get the current + tool shed and latest revision at the time of upload --> +<repository changeset_revision="627c7b41b970" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.tar.gz |
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| Binary file tools/filters/seq_rename.tar.gz has changed |
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| diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.txt --- a/tools/filters/seq_rename.txt Wed May 08 13:25:12 2013 -0400 +++ b/tools/filters/seq_rename.txt Mon Jun 24 01:59:15 2013 -0400 |
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| @@ -23,14 +23,15 @@ Automated Installation ====================== -This should be straightforward, provided you have installed Biopython 1.54 or later. -Galaxy should automatically install the Python script, and run the unit tests. +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. Manual Installation =================== -There are just two files to install: +There are just two files to install to use this tool from within Galaxy: * seq_rename.py (the Python script) * seq_rename.xml (the Galaxy tool definition) @@ -59,6 +60,7 @@ - Add unit test. - Check for errors using Python script's return code. v0.0.3 - Link to Tool Shed added to help text and this documentation. +v0.0.4 - Automated installation of Biopython dependency. Developers @@ -70,7 +72,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta +$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* tools/filters/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta Check this worked: |
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| diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.xml --- a/tools/filters/seq_rename.xml Wed May 08 13:25:12 2013 -0400 +++ b/tools/filters/seq_rename.xml Mon Jun 24 01:59:15 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.3"> +<tool id="seq_rename" name="Rename sequences" version="0.0.4"> <description>with ID mapping from a tabular file</description> <version_commmand interpreter="python">seq_rename.py --version</version_commmand> <command interpreter="python"> |